Transilice - Effects of silicon (Si) supply on leaf and root transcriptomes
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ABSTRACT:
ORGANISM(S): Brassica napus
PROVIDER: GSE122968 | GEO | 2019/02/22
REPOSITORIES: GEO
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Project description:transilice - Effects of silicon (Si) supply on leaf and root transcriptomes
| PRJNA507014 | ENA
Project description:The supply of soluble silicon (Si) to plants has been associated with many benefits that remain poorly explained and often contested. In this work, the effect of Si was studied on wheat plants under both control and pathogen stress (Blumeria graminis f.sp. tritici (Bgt)) conditions by conducting an exhaustive transcriptomic analysis (55,000 genes) aimed at comparing the differential response of plants under four treatments. The response to the supply of Si on control (uninfected) plants was limited to 47 genes providing little evidence of regulation of a specific metabolic process. Plants reacted to inoculation with Bgt by an up-regulation of many genes linked to stress and metabolic processes and a down-regulation of genes linked to photosynthesis. Supplying Si to inoculated plants largely prevented disease development, a phenotypic response that translated into a nearly perfect reversal of genes regulated by the effect of Bgt alone. These results suggest that Si plays a limited role on a plantâs metabolism in absence of stress, even in the case of a high-Si accumulating monocot such as wheat. On the other hand, the benefits of Si, in the form of biotic stress alleviation, were remarkably aligned with a counter-response to transcriptomic changes induced by the pathogen Bgt. Experiment Overall Design: Wheat culture in hydroponic system : Experiment Overall Design: Hydroponic systems were used to precisely control Si feeding of plants and to reduce external Si contamination. Seeds of wheat cultivar AC Drummond, chosen for its known high susceptibility to Bgt, were sown in 9-cm pots in a nylon bed consisting of nylon stockings cut into small ribbons. Hydroponic systems were set up to immerse roots for 15 minutes every 30 minutes. The plants were grown in a greenhouse (16 h light at 22°C and 8h dark at 18°C, 80% humidity). Plants were immersed in distilled water only during the first week following sowing. Experiment Overall Design: Si amendment and Bgt inoculation: Experiment Overall Design: Wheat plants were grown in the presence (Si+) or absence (Si-) of Si and inoculated (B+) or not (B-) with Bgt for a total of four treatments: Si-B-, Si+B-, Si-B+, and Si+B+. These treatments were applied in the following manner. One week after sowing, distilled water was replaced by a Hoagland solution amended or not with potassium silicate (Kasil 6, PQ Corp etc) at a concentration of 1.7 mM (Si+ Hoagland). Twice a week, Si was added to the Si+ nutrient solution in order to maintain Si concentration at 1.7 mM. Every other week, both Si- and Si+ Hoagland solutions were renewed and the pH adjusted to 5.8 in all systems at each Si addition or nutrient solution renewal. Experiment Overall Design: Four weeks after sowing (i.e. three weeks after Si amendment started), half the plants were inoculated with Bgt as described previously. Briefly, one day prior to inoculation, reservoir wheat plants heavily infected with Bgt were gently shaken to remove old spores and to stimulate the production of fresh ones. The inoculation was performed by shaking these infected wheat plants over the experimental plants . Experiment Overall Design: RNA preparation: Experiment Overall Design: Total RNA was extracted from leaves of three plants per treatment (three biological replicates) with the RNeasy plant kit (Qiagen, Hilden, Germany). Concentration and quality of RNA were assessed on a Nanodrop spectrophotometer (Nanodrop, Wilmington, De, USA) and 2100 Bioanalyzer (Agilent, Palo Alto, Ca, USA). Biotin-labeled cRNAs were synthesized using MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, Tx, USA) following the manufacturerâs instructions using 1 µg total RNA. Labelled cRNA was then fragmented using 5X Array Fragmentation Buffer supplied with the MessageAmp II-Biotin Enhanced Kit. Experiment Overall Design: Microarray hybridization: Experiment Overall Design: The labeled samples were added to an Affymetrix GeneChip® Wheat Genome Array (Affymetrix, Santa Clara, CA, USA), according to the manufacturerâs instructions. The wheat chip contains probe sets representing 55,052 transcripts for all 42 chromosomes in the wheat genome. The chips were hybridized for 16 h at 45 °C in a rotisserie oven at 60 rpm. Following hybridization, the arrays were washed and stained in an Affymetrix Fluidics Station 450, according to the standard protocol from Affymetrix, and scanned using an Affymetrix Scanner 3000. Twelve chips were prepared and corresponded to three biological replications of each of the four treatments (Si-B-, Si+B-, Si-B+, and Si+B+).
2009-07-04 | E-GEOD-12936 | biostudies-arrayexpress
Project description:The supply of soluble silicon (Si) to plants has been associated with many benefits that remain poorly explained and often contested. In this work, the effect of Si was studied on wheat plants under both control and pathogen stress (Blumeria graminis f.sp. tritici (Bgt)) conditions by conducting an exhaustive transcriptomic analysis (55,000 genes) aimed at comparing the differential response of plants under four treatments. The response to the supply of Si on control (uninfected) plants was limited to 47 genes providing little evidence of regulation of a specific metabolic process. Plants reacted to inoculation with Bgt by an up-regulation of many genes linked to stress and metabolic processes and a down-regulation of genes linked to photosynthesis. Supplying Si to inoculated plants largely prevented disease development, a phenotypic response that translated into a nearly perfect reversal of genes regulated by the effect of Bgt alone. These results suggest that Si plays a limited role on a plant’s metabolism in absence of stress, even in the case of a high-Si accumulating monocot such as wheat. On the other hand, the benefits of Si, in the form of biotic stress alleviation, were remarkably aligned with a counter-response to transcriptomic changes induced by the pathogen Bgt. Keywords: stress type and molecule effect
2009-06-30 | GSE12936 | GEO
Project description:The metabolic response of maize source leaves to low nitrogen supply was analyzed in maize seedlings by parallel measurements of transcriptome and metabolome profiling. Inbred lines A188 and B73 were cultivated under controlled growth chamber conditions and supplied with either sufficient (15mM) or limiting (0.15mM) nitrate supply. Leaf lamina material was harvested at day 20 and day 30 after germination with the fifth and sixth leaf representing the main source leaf respectively. Four replicates were collecetd from individual plants for each combination of genotype, growth stage and nitrogen treatment. The leaf material was frozen, homogenised and aliquoted for transcriptome and metabolome analysis. The molecular data was further supplemented by phenotypic characterisation of the maize seedlings under investigation. Limited availability of nitrogen caused strong shifts in the metabolite profile of leaves. The transcriptome was less affected by the nitrogen stress but showed strong genotype and age dependent patterns. Nitrogen starvation initiated the selective down-regulation of processes involved in nitrate reduction and amino acid assimilation; ammonium assimilation related transcripts on the other hand were not influenced. Carbon assimilation related transcripts were characterized by high transcriptional coordination and general down-regulation under low nitrogen conditions. Nitrogen deprivation caused a slight accumulation of starch, but also directed increased amounts of carbohydrates into the cell wall and secondary metabolites. The decrease in N availability also resulted in accumulation of phosphate and by strong down-regulation of genes usually involved in phosphate starvation response, underlining the great importance of phosphate homeostasis control under stress conditions. Maize inbred lines A188 and B73 were cultivated in pots containing nutrient poor peat soil under the controlled conditions of a growth chamber. The plants were fertilized with modified Hoagland solutions containing either 15mM (high N) or 0.15mM nitrate (low N). Source leaf lamina were harvested at day 20 and day 30 after start of germination for parallel analysis of transcriptome and metabolome profiles. The molecular data is further supplemented by phenotypic characterization of the maize seedlings under investigation.
2012-11-01 | E-GEOD-40678 | biostudies-arrayexpress
Project description:Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes.
2009-05-03 | GSE15915 | GEO
Project description:Shoot zinc (Zn) in Brassica oleracea is affected by soil Zn and phosphorus (P) concentrations. Most problematic is the negative impact of P fertilizers on Zn concentrations in crops, which makes balancing yield and mineral quality challenging. To evaluate molecular mechanisms involved in the accumulation of large shoot Zn concentrations regardless of the P supply, two B. oleracea accessions were grown hydroponically for two weeks with different combination of P and Zn supply. Ionome profiling and deep RNA sequencing of roots revealed interactions of P and Zn in planta, without apparent phenotypic effects. In addition, increasing P supply did not reduce tissue Zn concentration. Substantial changes in gene expression in roots of both accessions ensured nutritionally sufficient P and Zn uptake. Numerous genes were differentially expressed after changing Zn or P supply and most of them were unique to only one accession, highlighting different strategies in achieving nutrient sufficiency. Thus, different gene networks responded to the changing P and Zn supply in the two accessions. Additionally, enrichment analysis of gene ontology classes revealed that genes involved in lipid metabolism, response to starvation, and anion transport mechanisms were most responsive to the contrasting P and Zn supply in both accessions. The results agreed with previously studies demonstrating alterations in P transport and phospholipid metabolism in response to reduced P supply. Knowledge of genes responsive to P or Zn supply will help illuminate the interactions between these elements in their uptake and accumulation by plants and might highlight candidate genes for breeding high-yield-high-Zn crops.
2019-03-01 | GSE127467 | GEO
Project description:We investigated the effects of extracellular silicic acid on the whole Phaeodactylum triconutum transcriptome. In this work, global transcription analyses were combined with comparative studies of other elements, and detailed analyses of the silicon transporters. Our results provide insight on Si-sensing genes and further extend current models for Si uptake. Keywords: Comparative transcriptome analyses from Phaeodactylum triconutum fusiform cells acclimated in a Si-free or silicic acid medium.
2009-09-29 | GSE12015 | GEO
Project description:Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes. Four-condition experiment, comparison of transcription profiles of the genomes. Four biological replicates were used, independently grown and harvested. One replicate per array.
2010-05-19 | E-GEOD-15915 | biostudies-arrayexpress
Project description:Purpose: to find the potential down-stream target gene of circFAM120A Methods: mRNA profiles of decidualized human endometrial stromal cells (hESCs) after down-regulated FAM120A and control using siRNA were generated by NGS and compared by bioinformatics analysis Results: we sequenced 26414 mRNAs in hESCs between the si-NC and si-circFAM120A groups and identified 242 differentially expressed mRNAs, between which 161 were downregulated and 81 were up-regulated in si-circFAM120A group Conclusions: Our study represents the detailed analysis of decidualized hESCs transcriptomes between si-NC and si-circFAM120A groups.
2023-06-30 | GSE174495 | GEO
Project description:mRNA expression profiling of the embryo, endosperm (micropylar, peripheral, chalazal), and seed coat (outer, inner, chalazal, chalazal proliferating tissue) of the developing Brassica napus seed. Tissues were isolated using laser microdissection (LMD) from Brassica napus seeds at the globular, heart, and mature green stages of seed development.
2024-07-15 | GSE271809 | GEO